+Open data
-Basic information
Entry | Database: PDB / ID: 4k3r | ||||||
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Title | E. coli sliding clamp in complex with AcQLDLA | ||||||
Components |
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Keywords | TRANSFERASE / E. coli sliding clamp | ||||||
Function / homology | Function and homology information Hda-beta clamp complex / bacterial-type DNA replication / replication inhibiting complex / DNA polymerase III complex / replisome / regulation of DNA-templated DNA replication initiation / DNA strand elongation involved in DNA replication / error-prone translesion synthesis / negative regulation of DNA-templated DNA replication initiation / 3'-5' exonuclease activity ...Hda-beta clamp complex / bacterial-type DNA replication / replication inhibiting complex / DNA polymerase III complex / replisome / regulation of DNA-templated DNA replication initiation / DNA strand elongation involved in DNA replication / error-prone translesion synthesis / negative regulation of DNA-templated DNA replication initiation / 3'-5' exonuclease activity / DNA-templated DNA replication / DNA-directed DNA polymerase activity / DNA damage response / protein homodimerization activity / DNA binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.86 Å | ||||||
Authors | Yin, Z. / Oakley, A.J. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2013 Title: Structural and Thermodynamic Dissection of Linear Motif Recognition by the E. coli Sliding Clamp Authors: Yin, Z. / Kelso, M.J. / Beck, J.L. / Oakley, A.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4k3r.cif.gz | 166 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4k3r.ent.gz | 128.3 KB | Display | PDB format |
PDBx/mmJSON format | 4k3r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k3/4k3r ftp://data.pdbj.org/pub/pdb/validation_reports/k3/4k3r | HTTPS FTP |
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-Related structure data
Related structure data | 4k3kC 4k3lC 4k3mC 4k3oC 4k3pC 4k3qC 4k3sC 1mmiS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein / Protein/peptide , 2 types, 3 molecules ABE
#1: Protein | Mass: 40630.508 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: DnaN / Plasmid: pND261 / Production host: Escherichia coli (E. coli) / Strain (production host): AN1459 / References: UniProt: P0A988, DNA-directed DNA polymerase #2: Protein/peptide | ( | Mass: 584.663 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthesized peptide |
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-Non-polymers , 6 types, 566 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-PGE / | #6: Chemical | ChemComp-CL / | #7: Chemical | ChemComp-PG4 / | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.46 % / Mosaicity: 1.35 ° |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 100mM MES, 100-150mM CaCl2, 25-30%(v/v) PEG400, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 6, 2012 / Details: mirrors | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.859→74.265 Å / Num. all: 61020 / Num. obs: 61020 / % possible obs: 92.5 % / Observed criterion σ(F): -2 / Observed criterion σ(I): -2 / Redundancy: 3.1 % / Rsym value: 0.06 / Net I/σ(I): 9.7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1MMI Resolution: 1.86→43.98 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.92 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 3.937 / SU ML: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.176 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 73.08 Å2 / Biso mean: 29.7885 Å2 / Biso min: 15.3 Å2
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Refinement step | Cycle: LAST / Resolution: 1.86→43.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.859→1.907 Å / Total num. of bins used: 20
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